Computational Methods for 3D Genome Analysis
| Corporate Author: | |
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| Other Authors: | |
| Summary: | XIII, 457 p. 79 illus., 78 illus. in color. text |
| Language: | English |
| Published: |
New York, NY :
Springer US : Imprint: Humana,
2025.
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| Edition: | 1st ed. 2025. |
| Series: | Methods in Molecular Biology,
2856 |
| Subjects: | |
| Online Access: | https://doi.org/10.1007/978-1-0716-4136-1 |
| Format: | Electronic eBook |
Table of Contents:
- Methods for Genome-Wide Chromatin Interaction Analysis
- Structural Maintenance of Chromosomes Complexes
- Read Mapping for Hi-C Analysis
- Micro-C Analysis Workflow using Pairtools and Juicer
- HOMER for Analysis of Hi-C Data and Assessment of Composite Structure of the X Chromosome
- CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices
- Acquisition and Analysis Methods for Hi-C Data from Medaka Early Embryos
- Step-by-Step Protocol to Generate Hi-C Contact Maps Using the rfy_hic2 Pipeline
- Hi-C/3C-seq Data Analysis for Prokaryotic Genomes with HiC-Pro
- Exploring Contact Distance Distributions with Google Colaboratory
- Supervised Chromatin Loop Detection using Peakachu Version 2
- Systematic Inference of Multi-Scale Chromatin Sub-Compartments using Calder2
- Analysis and Visualization of Multiple Hi-C and Micro-C Data with CustardPy
- Single-Cell Hi-C Analysis Workflow with Pairtools
- Reconstruction of 3D Chromosome Structure from Single Cell Hi-C Data via Recurrence Plots
- 4D Genome Analysis using PHi-C2
- Construction of Coarse-Grained Molecular Dynamics Model of Nuclear Global Chromosomes Dynamics in Mammalian Cells
- Three-Dimensional Simulation of Whole-Genome Structuring through the Transition from Anaphase to Interphase
- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference
- Prediction of Enhancer-Gene Interactions using Chromatin-Conformation Capture and Epigenome Data using STARE
- Learning Enhancer-Gene Associations from Bulk Transcriptomic and Epigenetic Sequencing Data with STITCHIT
- Machine and Deep Learning Methods for Predicting 3D Genome Organization
- Processing and Visualization of Protec-Seq Data for the Generation of Calibrated, Genome-Wide Double DSB (Double Strand Break) Maps
- Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH Data
- Extracting Chromosome Structural Information as One-Dimensional Metrics and Integrating Them with Epigenomics
- Exploring Cohesin-Related Multiomics Information in the Web Browser.